Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold215
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2124891
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 13 of 16
Found at i:1473827 original size:20 final size:19
Alignment explanation
Indices: 1473780--1473833 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1473770 ACATTATGCT
**
1473780 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGCACA
1473799 TTGTATCGATACATGCACAA
1 TTGTATCGATACATGCAC-A
*
1473819 TTTTATCGATACATG
1 TTGTATCGATACATG
1473834 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATGCACA
Found at i:1474550 original size:51 final size:51
Alignment explanation
Indices: 1474474--1474610 Score: 256
Period size: 51 Copynumber: 2.7 Consensus size: 51
1474464 ACATGTATGA
*
1474474 ATGTATCGATACATTCTTTAATGTATCGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCAG
1474525 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCAG
1 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCAG
*
1474576 ATGTATCGATACATTTTTCAATGTATCGATACATT
1 ATGTATCGATACATTCTTCAATGTATCGATACATT
1474611 TAGTTAAAAT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 84 1.00
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.42
Consensus pattern (51 bp):
ATGTATCGATACATTCTTCAATGTATCGATACATTCTATCTTTTTACCCAG
Found at i:1474566 original size:24 final size:20
Alignment explanation
Indices: 1474434--1474561 Score: 105
Period size: 20 Copynumber: 5.8 Consensus size: 20
1474424 AAGTTCCCAG
*
1474434 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* *
1474454 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
1474474 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATTCTTCA
1474494 ATGTATCGATACATTCTATCTTTTTACCCA
1 ATGTATCGATACA---T-TC---TT---CA
1474524 GATGTATCGATACATTCTTCA
1 -ATGTATCGATACATTCTTCA
1474545 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1474562 ATCTTTTTAC
Statistics
Matches: 90, Mismatches: 5, Indels: 26
0.74 0.04 0.21
Matches are distributed among these distances:
19 1 0.01
20 62 0.69
21 3 0.03
23 1 0.01
24 4 0.04
27 4 0.04
28 1 0.01
30 1 0.01
31 13 0.14
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1489865 original size:28 final size:28
Alignment explanation
Indices: 1489825--1490442 Score: 758
Period size: 28 Copynumber: 21.8 Consensus size: 28
1489815 CTAGAACGTT
* *
1489825 CATCATTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
*
1489853 CATCCTTTCAAAGCCCACAAGTCAATGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
*
1489881 CACCCTATT-AAAGCCCACAAGTCAGTGG
1 CATCCT-TTCAAAGCCCACAAGTCAGTGG
* *
1489909 CACCCTTTCAAAGCCCACAAGTCAGTAG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
*
1489937 CACTCTTTTCAAAGCCCACAAGTCAGTGG
1 CA-TCCTTTCAAAGCCCACAAGTCAGTGG
* * *
1489966 CATCCTTTCAAAGCCCACAATTTAATGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
* * **
1489994 CACCCTTTTAAAGCCTGCAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
* *
1490022 CA-CTCTATTCAAAGCCCACACGAGTCGGTAG
1 CATC-CT-TTCAAAGCCCACA--AGTCAGTGG
*
1490053 CAACTCTTTTCAAAGCCCACAAGTCAGTGG
1 C-A-TCCTTTCAAAGCCCACAAGTCAGTGG
* *
1490083 CATCCTTTCAAAGCCCACGAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
* *
1490111 CACCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
*
1490139 CA-CCATTTCAAAGCCCCCAAGTCAGTGG
1 CATCC-TTTCAAAGCCCACAAGTCAGTGG
* * *
1490167 CACTCTTTTCAAAGTCCACAAGTCAGTAG
1 CA-TCCTTTCAAAGCCCACAAGTCAGTGG
1490196 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
* *
1490224 CAACCTATCAAAGCCCACAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
* *
1490252 CA-CCTTTTCAAAGCCCATAAGTTAGTGG
1 CATCC-TTTCAAAGCCCACAAGTCAGTGG
*
1490280 CACTCTTTTCAAAGCCCACAAGTCAGTGG
1 CA-TCCTTTCAAAGCCCACAAGTCAGTGG
* *
1490309 CATTCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
*
1490337 CACCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
*
1490365 CATCCTTTCAAAGCCCACAAATCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
* *
1490393 CACCCTTTCAAAGCCCACAAATCAGTGG
1 CATCCTTTCAAAGCCCACAAGTCAGTGG
*
1490421 CACTCTTTTCAAAGCCCACAAG
1 CA-TCCTTTCAAAGCCCACAAG
1490443 CCAATGGTAA
Statistics
Matches: 511, Mismatches: 62, Indels: 33
0.84 0.10 0.05
Matches are distributed among these distances:
27 7 0.01
28 371 0.73
29 99 0.19
30 10 0.02
31 8 0.02
32 14 0.03
33 1 0.00
34 1 0.00
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (28 bp):
CATCCTTTCAAAGCCCACAAGTCAGTGG
Found at i:1489959 original size:85 final size:85
Alignment explanation
Indices: 1489830--1490442 Score: 797
Period size: 85 Copynumber: 7.2 Consensus size: 85
1489820 ACGTTCATCA
* *
1489830 TTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAATGGCACCCTATT-AAA
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT-TTCAAA
1489893 GCCCACAAGTCAGTGGCACCC
65 GCCCACAAGTCAGTGGCACCC
* * *
1489914 TTTCAAAGCCCACAAGTCAGTAGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* * *
1489979 CCCACAATTTAATGGCACCC
66 CCCACAAGTCAGTGGCACCC
* ** * * *
1489999 TTTTAAAGCCTGCAAGTCAGTGGCACT-CTATTCAAAGCCCACACGAGTCGGTAGCAACTCTTTT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCT-TTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTT
*
1490063 CAAAGCCCACAAGTCAGTGGCATCC
61 CAAAGCCCACAAGTCAGTGGCACCC
* * * *
1490088 TTTCAAAGCCCACGAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACCATTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* *
1490152 CCCCCAAGTCAGTGGCACTCT
66 CCCACAAGTCAGTGGCAC-CC
* * * *
1490173 TTTCAAAGTCCACAAGTCAGTAGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCAACCTATCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
*
1490237 CCCACAAGTCAGTGGCACCT
66 CCCACAAGTCAGTGGCACCC
* * * **
1490257 TTTCAAAGCCCATAAGTTAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCATTCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
*
1490322 CCCACAAGTTAGTGGCACCC
66 CCCACAAGTCAGTGGCACCC
*
1490342 TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAATCAGTGGCACCCTTTCAAAG
1 TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
* *
1490406 CCCACAAATCAGTGGCACTCT
66 CCCACAAGTCAGTGGCAC-CC
1490427 TTTCAAAGCCCACAAG
1 TTTCAAAGCCCACAAG
1490443 CCAATGGTAA
Statistics
Matches: 456, Mismatches: 61, Indels: 23
0.84 0.11 0.04
Matches are distributed among these distances:
84 125 0.27
85 254 0.56
86 7 0.02
87 8 0.02
88 14 0.03
89 48 0.11
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (85 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAG
CCCACAAGTCAGTGGCACCC
Found at i:1490223 original size:113 final size:112
Alignment explanation
Indices: 1489830--1490442 Score: 879
Period size: 113 Copynumber: 5.4 Consensus size: 112
1489820 ACGTTCATCA
* * *
1489830 TTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCACCCTATT-AAAG
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCT-TTCAAAG
*
1489894 CCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTAGCACTCT
65 CCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1489943 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAATTTAATGGCACCCTTTTAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
** * *
1490008 CTGCAAGTCAGTGGCACTCTATTCAAAGCCCACACGAGTCGGTAGCAACTCT
66 CCACAAGTCAGTGGCAC-CT-TTCAAAGCCCACA--AGTCAGTGGC-ACTCT
*
1490060 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGAGTTAGTGGCACCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
* *
1490125 CCACAAGTTAGTGGCACCATTTCAAAGCCCCCAAGTCAGTGGCACTCT
66 CCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * * *
1490173 TTTCAAAGTCCACAAGTCAGTAGCATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTATCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
* *
1490238 CCACAAGTCAGTGGCACCTTTTCAAAGCCCATAAGTTAGTGGCACTCT
66 CCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1490286 TTTCAAAGCCCACAAGTCAGTGGCATTCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
* *
1490351 CCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAATCAGTGGCAC-CC
66 CCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1490398 TTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAG
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAG
1490443 CCAATGGTAA
Statistics
Matches: 451, Mismatches: 40, Indels: 18
0.89 0.08 0.04
Matches are distributed among these distances:
112 28 0.06
113 297 0.66
114 23 0.05
116 22 0.05
117 81 0.18
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (112 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
CCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:1496506 original size:21 final size:21
Alignment explanation
Indices: 1496482--1496522 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1496472 TTTTAAAAAA
*
1496482 TTCATTTATTTT-TTTAAATTT
1 TTCATTT-TTTTCTTGAAATTT
1496503 TTCATTTTTTTCTTGAAATT
1 TTCATTTTTTTCTTGAAATT
1496523 CTCTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.68
Consensus pattern (21 bp):
TTCATTTTTTTCTTGAAATTT
Found at i:1496673 original size:21 final size:20
Alignment explanation
Indices: 1496649--1496691 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1496639 TTTTGAAAAA
* *
1496649 TTTATTTATTTTCTTGAATTT
1 TTTATTT-TTTCCTTGAAATT
1496670 TTTATTTTTTCCTTGAAATT
1 TTTATTTTTTCCTTGAAATT
1496690 TT
1 TT
1496692 CCTATTTCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTATTTTTTCCTTGAAATT
Found at i:1496686 original size:20 final size:22
Alignment explanation
Indices: 1496649--1496691 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1496639 TTTTGAAAAA
*
1496649 TTTATTTATTTTCTTG-AATTT
1 TTTATTTATTTCCTTGAAATTT
1496670 TTTATTT-TTTCCTTGAAATTT
1 TTTATTTATTTCCTTGAAATTT
1496691 T
1 T
1496692 CCTATTTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.19, C:0.07, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTATTTATTTCCTTGAAATTT
Found at i:1496834 original size:165 final size:167
Alignment explanation
Indices: 1496370--1496844 Score: 554
Period size: 165 Copynumber: 2.9 Consensus size: 167
1496360 ATTGTTCTTG
* * * * *
1496370 AAAAATTA-AGTTTTCTAT-TCCATAAATGTTTTCG-GAGCGATTTTTCTCAGTTTAAAATTTTT
1 AAAAAATAGAGTTTTCT-TCTCCATAAATTTTTTTGAGGGGGATTTTTCTCAGTTTAAAATTTTT
* * * * * *
1496432 AAAATTCATCTAACATTGTCGTT-AATTCATATTAAATCAGTTTTAAAAAATTCATTTATTTTTT
65 AAAATTCATCTAATATTGTCATTAAATTTATATTAAATCAGTTTTTAAAAATTTATTTATTTTAT
* * * * **
1496496 TAAATTTTTCATTTTTTTCTTGAAATTCTCTTATTTTT
130 TGAATTTTTAATTTTTTCCTTGAAATTCTCCTATTTCC
* *
1496534 AAAAAATAGAGTTTTCTTCTCCATAAATTTTTTTGAGGGGGATATTTCTCGAG-TTAAAAATTTT
1 AAAAAATAGAGTTTTCTTCTCCATAAATTTTTTTGAGGGGGATTTTTCTC-AGTTTAAAATTTTT
* * * * * *
1496598 AAAATTCATCTAATATTATTAATAAATTTATATTAAATTAGTTTTGAAAAATTTATTTATTTTCT
65 AAAATTCATCTAATATTGTCATTAAATTTATATTAAATCAGTTTTTAAAAATTTATTTATTTTAT
* *
1496663 TGAATTTTTTATTTTTTCCTTGAAATTTTCCTATTTCC
130 TGAATTTTTAATTTTTTCCTTGAAATTCTCCTATTTCC
*
1496701 CAAAAATAGA-TTCTTCTTCTCCAT-AATTTTTTTG-GGGGGATTTTTCTCAGTTTAAAATTTTT
1 AAAAAATAGAGTT-TTCTTCTCCATAAATTTTTTTGAGGGGGATTTTTCTCAGTTTAAAATTTTT
* * *
1496763 AAAATTCATTTAATATTGTCATTAAATTTGTATTAAATCAGTTTTTAAAAATTTAAATTA-TTTA
65 AAAATTCATCTAATATTGTCATTAAATTTATATTAAATCAGTTTTTAAAAATTT-ATTTATTTTA
* *
1496827 ATGAATTTTGAATTTTTT
129 TTGAATTTTTAATTTTTT
1496845 GTATTTATTG
Statistics
Matches: 264, Mismatches: 39, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
164 10 0.04
165 110 0.42
166 55 0.21
167 89 0.34
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.50
Consensus pattern (167 bp):
AAAAAATAGAGTTTTCTTCTCCATAAATTTTTTTGAGGGGGATTTTTCTCAGTTTAAAATTTTTA
AAATTCATCTAATATTGTCATTAAATTTATATTAAATCAGTTTTTAAAAATTTATTTATTTTATT
GAATTTTTAATTTTTTCCTTGAAATTCTCCTATTTCC
Found at i:1497215 original size:17 final size:17
Alignment explanation
Indices: 1497195--1497227 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1497185 CATGAAAATT
1497195 GAAAAA-TAAAGAAAAAA
1 GAAAAATTAAA-AAAAAA
1497212 GAAAAATTAAAAAAAA
1 GAAAAATTAAAAAAAA
1497228 TTAGTGGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
GAAAAATTAAAAAAAAA
Found at i:1498147 original size:23 final size:22
Alignment explanation
Indices: 1498109--1498151 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1498099 CAATTTTTGA
1498109 AAATAAATAATAATAATAATAAT
1 AAATAAATAATAATAA-AATAAT
1498132 AAATAAATAA-ATATAAAATA
1 AAATAAATAATA-ATAAAATA
1498152 TTATTCTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAAATAATAATAAAATAAT
Found at i:1499406 original size:32 final size:32
Alignment explanation
Indices: 1499288--1499414 Score: 145
Period size: 32 Copynumber: 3.9 Consensus size: 32
1499278 CCTTACAACA
1499288 CTATC-TTTCAAGGCTAAGATAGAAACC--TCC
1 CTATCTTTTCAAGGCTAAGATAG-AACCTTTCC
* *
1499318 CTATCTTTTCACGGGCCAAGATAGAACCTTTCTC
1 CTATCTTTTCA-AGGCTAAGATAGAACCTTTC-C
1499352 CTTATCTTTTACAAAGGCTAAGATAGAACCTTATCC
1 C-TATCTTTT-C-AAGGCTAAGATAGAACCTT-TCC
1499388 CTATC-TTTCAAGGCTAAGATAGAACCT
1 CTATCTTTTCAAGGCTAAGATAGAACCT
1499415 CTCAATCACT
Statistics
Matches: 84, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
30 5 0.06
31 9 0.11
32 28 0.33
33 3 0.04
34 5 0.06
35 12 0.14
36 19 0.23
37 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (32 bp):
CTATCTTTTCAAGGCTAAGATAGAACCTTTCC
Found at i:1499985 original size:19 final size:19
Alignment explanation
Indices: 1499942--1500015 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 19
1499932 CACACCCAGA
* *
1499942 TGTATCGATACATTATGCTT
1 TGTATCGATACATGAT-CAT
1499962 TGTATCGATACATGATCAT
1 TGTATCGATACATGATCAT
1499981 TGTATCGATACATGGA-CAAT
1 TGTATCGATACAT-GATC-AT
1500001 TGTATCGATACATGA
1 TGTATCGATACATGA
1500016 AACTAGCAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 18 0.36
20 32 0.64
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:1500103 original size:33 final size:32
Alignment explanation
Indices: 1500044--1500107 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
1500034 TACCACTGTT
1500044 TATATCGATACATAGATATTGTATCGATACAA
1 TATATCGATACATAGATATTGTATCGATACAA
1500076 TATATCGATACAT-GATGAATTGTATCGATACA
1 TATATCGATACATAGAT--ATTGTATCGATACA
1500108 TTGCTTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 3 0.10
32 13 0.43
33 14 0.47
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (32 bp):
TATATCGATACATAGATATTGTATCGATACAA
Found at i:1504038 original size:20 final size:19
Alignment explanation
Indices: 1503988--1504046 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1503978 ATCGATCGAT
*
1503988 ACATTATATCGATACGTGA
1 ACATTATATCGATACATGA
*
1504007 TCATTATATCGATACATGA
1 ACATTATATCGATACATGA
* *
1504026 ACAATTGTATCGATATATGA
1 AC-ATTATATCGATACATGA
1504046 A
1 A
1504047 ACTGGCAGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (19 bp):
ACATTATATCGATACATGA
Found at i:1504133 original size:33 final size:32
Alignment explanation
Indices: 1504074--1504135 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
1504064 TACCACTGTT
*
1504074 TGTATCGATACATGGACATTGTATCGATACAA
1 TGTATCAATACATGGACATTGTATCGATACAA
1504106 TGTATCAATACATGATGA-ATTGTATCGATA
1 TGTATCAATACATG--GACATTGTATCGATA
1504136 TATTGCTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 13 0.48
33 12 0.44
34 2 0.07
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCAATACATGGACATTGTATCGATACAA
Found at i:1505155 original size:22 final size:22
Alignment explanation
Indices: 1505127--1505185 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
1505117 ATGAACAGTG
1505127 ATGAATAGTGATG-AACAAATAC
1 ATGAATAGTGATGTAAC-AATAC
* *
1505149 ATGAATAGTGATGTATCGATAC
1 ATGAATAGTGATGTAACAATAC
*
1505171 ATGAACAGTGATGTA
1 ATGAATAGTGATGTA
1505186 TTGTTACAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 31 0.94
23 2 0.06
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.27
Consensus pattern (22 bp):
ATGAATAGTGATGTAACAATAC
Found at i:1508474 original size:21 final size:21
Alignment explanation
Indices: 1508448--1508502 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1508438 TACTTGCAAC
*
1508448 TCATTTGTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
1508469 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
* *
1508490 TCACTTAATTTCT
1 TCATTTATTTTCT
1508503 TTTCAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.02, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:1508503 original size:21 final size:21
Alignment explanation
Indices: 1508463--1508506 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1508453 TGTTTTCTCC
* *
1508463 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
1508484 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
1508505 TC
1 TC
1508507 AAGAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:1510382 original size:13 final size:13
Alignment explanation
Indices: 1510364--1510390 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1510354 ACATTATGCT
1510364 TTGTATCGATACA
1 TTGTATCGATACA
1510377 TTGTATCGATACA
1 TTGTATCGATACA
1510390 T
1 T
1510391 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1510484 original size:20 final size:20
Alignment explanation
Indices: 1510459--1510524 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1510449 CTACCATTGT
1510459 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
1510479 TTGTATCGAT--AT---A-A
1 TTGTATCGATACATGGCACA
1510493 -TGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
1510512 TTGTATCGATACA
1 TTGTATCGATACA
1510525 ATGTATCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
15 3 0.08
18 3 0.08
19 1 0.03
20 22 0.56
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGGCACA
Found at i:1510497 original size:33 final size:33
Alignment explanation
Indices: 1510460--1510539 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1510450 TACCATTGTT
*
1510460 TGTATCGATACATGGCACATTGTATCGATATAA
1 TGTATCGATACATGGCACATTGTATCGATACAA
1510493 TGTATCGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATGGCACATTGTATCGATACAA
*
1510526 TGTATCAATACATG
1 TGTATCGATACATG
1510540 AAGAATTGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (33 bp):
TGTATCGATACATGGCACATTGTATCGATACAA
Found at i:1519312 original size:33 final size:33
Alignment explanation
Indices: 1519257--1519319 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
1519247 ACCACTATTT
** * *
1519257 TATCGATACATGGCGCACTGTATGGATACAATG
1 TATCGATACATGAAGAACTGTATCGATACAATG
*
1519290 TATCGATACATGAAGAATTGTATCGATACA
1 TATCGATACATGAAGAACTGTATCGATACA
1519320 TTGACTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (33 bp):
TATCGATACATGAAGAACTGTATCGATACAATG
Found at i:1520101 original size:32 final size:32
Alignment explanation
Indices: 1520062--1520216 Score: 147
Period size: 36 Copynumber: 4.6 Consensus size: 32
1520052 ACTATCTTTC
*
1520062 AAGGCTAAGATAGAAACCTCCCTATCTATT-CA
1 AAGGCTAAGATAG-AACCTCCCTATCTTTTACA
**
1520094 CGGGCTAAGATAGAACCTTTTTCCCTATCTTTTACA
1 AAGGCTAAGATAGAACC----TCCCTATCTTTTACA
1520130 AAGGCTAAGATAGAACCTTTCTCCCTATCTTTTACA
1 AAGGCTAAGATAGAA-C---CTCCCTATCTTTTACA
1520166 AAGGCTAAGATAGAACCTTATCCCTATC-TTT-C-
1 AAGGCTAAGATAGAACC---TCCCTATCTTTTACA
1520198 AAGGCTAAGATAGAACCTC
1 AAGGCTAAGATAGAACCTC
1520217 TCAATCACTT
Statistics
Matches: 106, Mismatches: 5, Indels: 27
0.77 0.04 0.20
Matches are distributed among these distances:
29 2 0.02
31 4 0.04
32 29 0.27
33 1 0.01
34 3 0.03
35 20 0.19
36 45 0.42
37 1 0.01
40 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (32 bp):
AAGGCTAAGATAGAACCTCCCTATCTTTTACA
Found at i:1520139 original size:68 final size:65
Alignment explanation
Indices: 1520053--1520216 Score: 206
Period size: 68 Copynumber: 2.4 Consensus size: 65
1520043 GAGCTTACAA
** *
1520053 CTATCTTTCAAGGCTAAGATAGAAACCTCCCTATCTATT-CACGGGCTAAGATAGAACCTTTTTC
1 CTATCTTTCAAGGCTAAGATAGAAACCTCCCTATCTATTACAAAGGCTAAGATAGAACC-TTATC
1520117 C
65 C
* *
1520118 CTATCTTTTACAAAGGCTAAGATAGAACCTTTCTCCCTATCTTTTACAAAGGCTAAGATAGAACC
1 CTATC-TTT-C-AAGGCTAAGATAGAAAC---CTCCCTATCTATTACAAAGGCTAAGATAGAACC
1520183 TTATCC
60 TTATCC
1520189 CTATCTTTCAAGGCTAAGATAG-AACCTC
1 CTATCTTTCAAGGCTAAGATAGAAACCTC
1520217 TCAATCACTT
Statistics
Matches: 86, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
64 3 0.03
65 5 0.06
66 3 0.03
67 3 0.03
68 29 0.34
69 1 0.01
70 3 0.03
71 22 0.26
72 17 0.20
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (65 bp):
CTATCTTTCAAGGCTAAGATAGAAACCTCCCTATCTATTACAAAGGCTAAGATAGAACCTTATCC
Found at i:1520140 original size:36 final size:36
Alignment explanation
Indices: 1520096--1520215 Score: 194
Period size: 36 Copynumber: 3.4 Consensus size: 36
1520086 TCTATTCACG
*
1520096 GGCTAAGATAGAACCTTTTTCCCTATCTTTTACAAA
1 GGCTAAGATAGAACCTTTATCCCTATCTTTTACAAA
*
1520132 GGCTAAGATAGAACCTTTCTCCCTATCTTTTACAAA
1 GGCTAAGATAGAACCTTTATCCCTATCTTTTACAAA
1520168 GGCTAAGATAGAACC-TTATCCCTATC-TTT-C-AA
1 GGCTAAGATAGAACCTTTATCCCTATCTTTTACAAA
1520200 GGCTAAGATAGAACCT
1 GGCTAAGATAGAACCT
1520216 CTCAATCACT
Statistics
Matches: 81, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
32 17 0.21
33 1 0.01
34 3 0.04
35 10 0.12
36 50 0.62
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (36 bp):
GGCTAAGATAGAACCTTTATCCCTATCTTTTACAAA
Found at i:1520712 original size:22 final size:22
Alignment explanation
Indices: 1520684--1520728 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1520674 ATAATGTATC
*
1520684 GATACATGAATAGTGATGAATA
1 GATACATGAACAGTGATGAATA
1520706 GATACATGAACAGTGATGAATA
1 GATACATGAACAGTGATGAATA
1520728 G
1 G
1520729 TGGTGTATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.24, T:0.24
Consensus pattern (22 bp):
GATACATGAACAGTGATGAATA
Found at i:1520730 original size:32 final size:32
Alignment explanation
Indices: 1520689--1520755 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
1520679 GTATCGATAC
*
1520689 ATGAATAGTGATGAATAGATACATGAACAGTG
1 ATGAATAGTGATGAATAGATACATGAACAATG
* * * *
1520721 ATGAATAGTGGTGTATCGATATATGAACAATG
1 ATGAATAGTGATGAATAGATACATGAACAATG
1520753 ATG
1 ATG
1520756 TATCGATACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.25, T:0.28
Consensus pattern (32 bp):
ATGAATAGTGATGAATAGATACATGAACAATG
Found at i:1527995 original size:13 final size:12
Alignment explanation
Indices: 1527955--1528033 Score: 59
Period size: 13 Copynumber: 7.2 Consensus size: 12
1527945 CTGCCAGTTT
1527955 CATGTATCGATA
1 CATGTATCGATA
*
1527967 CA-GT-T--ATC
1 CATGTATCGATA
1527975 CATGTATCGATA
1 CATGTATCGATA
1527987 CATTGTATCGAT-
1 CA-TGTATCGATA
*
1527999 -AT-AAT-GAT-
1 CATGTATCGATA
1528007 CATGTATCGATA
1 CATGTATCGATA
1528019 CATTGTATCGATA
1 CA-TGTATCGATA
1528032 CA
1 CA
1528034 AAGCATAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 19
0.70 0.05 0.25
Matches are distributed among these distances:
8 7 0.13
9 6 0.11
10 5 0.09
11 6 0.11
12 8 0.15
13 21 0.40
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (12 bp):
CATGTATCGATA
Found at i:1528016 original size:32 final size:32
Alignment explanation
Indices: 1527957--1528054 Score: 133
Period size: 33 Copynumber: 3.0 Consensus size: 32
1527947 GCCAGTTTCA
* *
1527957 TGTATCGATACAGTTATCCATGTATCGATACAT
1 TGTATCGATACAATGAT-CATGTATCGATACAT
*
1527990 TGTATCGATATAATGATCATGTATCGATACAT
1 TGTATCGATACAATGATCATGTATCGATACAT
* *
1528022 TGTATCGATACAAAGCATAATGTATCGATACAT
1 TGTATCGATACAATG-ATCATGTATCGATACAT
1528055 CTAGGTGTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 28 0.48
33 30 0.52
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAATGATCATGTATCGATACAT
Found at i:1530372 original size:20 final size:21
Alignment explanation
Indices: 1530342--1530387 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1530332 CTGTTTTTGT
1530342 TGAAGATTTTG-A-TGAAAAA
1 TGAAGATTTTGAAGTGAAAAA
1530361 TGAAGTATTTTGAAGTGAAAAA
1 TGAAG-ATTTTGAAGTGAAAAA
1530383 T-AAGA
1 TGAAGA
1530388 AATTTGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.21
20 7 0.29
21 4 0.17
22 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.30
Consensus pattern (21 bp):
TGAAGATTTTGAAGTGAAAAA
Found at i:1530392 original size:22 final size:20
Alignment explanation
Indices: 1530342--1530420 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 20
1530332 CTGTTTTTGT
1530342 TGAAG-ATTTTGATGAAAAA
1 TGAAGAATTTTGATGAAAAA
*
1530361 TGAAGTATTTTGAAGTGAAAAA
1 TGAAGAATTTTG-A-TGAAAAA
*
1530383 T-AAGAAATTTGA--AAAAGA
1 TGAAGAATTTTGATGAAAA-A
*
1530401 TTTGATGAATTTTGATGAAA
1 --TGAAGAATTTTGATGAAA
1530421 GGATGTTAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
17 4 0.09
18 1 0.02
19 5 0.11
20 8 0.17
21 18 0.38
22 8 0.17
23 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (20 bp):
TGAAGAATTTTGATGAAAAA
Found at i:1530393 original size:21 final size:22
Alignment explanation
Indices: 1530354--1530395 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1530344 AAGATTTTGA
* *
1530354 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
1530376 TGAAAAAT-AAGAAATTTGAA
1 TGAAAAATGAAGAAATTTGAA
1530396 AAAGATTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.29
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:1536773 original size:20 final size:20
Alignment explanation
Indices: 1536748--1536803 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
1536738 CAGTTTCATT
1536748 TATCGATACAATTATCCATG
1 TATCGATACAATTATCCATG
* *
1536768 TATCGATGCAATGAT-CATG
1 TATCGATACAATTATCCATG
*
1536787 TATCAATACAATGTATC
1 TATCGATACAAT-TATC
1536804 GATACAAAGC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (20 bp):
TATCGATACAATTATCCATG
Found at i:1536798 original size:19 final size:19
Alignment explanation
Indices: 1536743--1536799 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1536733 ACTGCCAGTT
* *
1536743 TCATTTATCGATACAATTA
1 TCATGTATCGATACAATGA
*
1536762 TCCATGTATCGATGCAATGA
1 T-CATGTATCGATACAATGA
*
1536782 TCATGTATCAATACAATG
1 TCATGTATCGATACAATG
1536800 TATCGATACA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:1536829 original size:33 final size:32
Alignment explanation
Indices: 1536765--1536829 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1536755 ACAATTATCC
* * *
1536765 ATGTATCGATGCAATGATCATGTATCAATACA
1 ATGTATCGATACAAAGATAATGTATCAATACA
*
1536797 ATGTATCGATACAAAGCATAATGTATCGATACA
1 ATGTATCGATACAAAG-ATAATGTATCAATACA
1536830 TCTAGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.29
Consensus pattern (32 bp):
ATGTATCGATACAAAGATAATGTATCAATACA
Found at i:1539204 original size:68 final size:68
Alignment explanation
Indices: 1539118--1539344 Score: 359
Period size: 68 Copynumber: 3.4 Consensus size: 68
1539108 AAACACTATC
* * * * *
1539118 TTTC-AAGGCTAAGATAGAAACCTCCCTATCTTCTCACGAGCTAAGAAAGAACCTCTCTCCCTAT
1 TTTCAAAGGCTAAGATAGAAACCTCCCTACCTTTTCATGGGCTAAGATAGAACCTCTCTCCCTAT
1539182 CTT
66 CTT
* *
1539185 TTTCAAAGGCTAAGGTAGAAACCTTCCTACCTTTTCATGGGCTAAGATAGAACCTCTCTCCCTAT
1 TTTCAAAGGCTAAGATAGAAACCTCCCTACCTTTTCATGGGCTAAGATAGAACCTCTCTCCCTAT
1539250 CTT
66 CTT
* *
1539253 TTTCAAAGGCTAAGATAGAACCCTCCCTACCTTTTCATGGGCTAAGATAGAACCTCTCTCTCTAT
1 TTTCAAAGGCTAAGATAGAAACCTCCCTACCTTTTCATGGGCTAAGATAGAACCTCTCTCCCTAT
1539318 CTT
66 CTT
1539321 TTTCAAAGGCTAAGATAG-AACCTC
1 TTTCAAAGGCTAAGATAGAAACCTC
1539345 TCAATCACTT
Statistics
Matches: 147, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
67 9 0.06
68 138 0.94
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (68 bp):
TTTCAAAGGCTAAGATAGAAACCTCCCTACCTTTTCATGGGCTAAGATAGAACCTCTCTCCCTAT
CTT
Found at i:1539264 original size:36 final size:36
Alignment explanation
Indices: 1539118--1539346 Score: 234
Period size: 36 Copynumber: 6.7 Consensus size: 36
1539108 AAACACTATC
*
1539118 TTTC-AAGGCTAAGATAGAA--AC-CTCCCTATC-T
1 TTTCAAAGGCTAAGATAGAACCTCTCTCCCTATCTT
* * *
1539149 TCTC-ACGAGCTAAGAAAGAACCTCTCTCCCTATCTT
1 TTTCAAAG-GCTAAGATAGAACCTCTCTCCCTATCTT
* * *
1539185 TTTCAAAGGCTAAGGTAGAAAC-CT-T-CCTA-CCT
1 TTTCAAAGGCTAAGATAGAACCTCTCTCCCTATCTT
**
1539217 TTTCATGGGCTAAGATAGAACCTCTCTCCCTATCTT
1 TTTCAAAGGCTAAGATAGAACCTCTCTCCCTATCTT
*
1539253 TTTCAAAGGCTAAGATAGAA-C-C-CTCCCTA-CCT
1 TTTCAAAGGCTAAGATAGAACCTCTCTCCCTATCTT
** *
1539285 TTTCATGGGCTAAGATAGAACCTCTCTCTCTATCTT
1 TTTCAAAGGCTAAGATAGAACCTCTCTCCCTATCTT
1539321 TTTCAAAGGCTAAGATAGAACCTCTC
1 TTTCAAAGGCTAAGATAGAACCTCTC
1539347 AATCACTTAG
Statistics
Matches: 160, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
31 5 0.03
32 51 0.32
33 14 0.09
34 5 0.03
35 22 0.14
36 61 0.38
37 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (36 bp):
TTTCAAAGGCTAAGATAGAACCTCTCTCCCTATCTT
Found at i:1539801 original size:20 final size:20
Alignment explanation
Indices: 1539776--1539830 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1539766 ATTGGGCTCA
1539776 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
*
1539796 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
*
1539816 ATGTGTCGATACAAT
1 ATGTATCGATACAAT
1539831 GTATCGATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:1539926 original size:13 final size:13
Alignment explanation
Indices: 1539908--1539932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1539898 TACCAAGAAC
1539908 ATGTATCGATACA
1 ATGTATCGATACA
1539921 ATGTATCGATAC
1 ATGTATCGATAC
1539933 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1539931 original size:32 final size:33
Alignment explanation
Indices: 1539890--1539953 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1539880 TATGTTAAGG
1539890 TGTATCGATACCAAG-AACATGTATCGATACAA
1 TGTATCGATACCAAGCAACATGTATCGATACAA
* *
1539922 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACCAAGCAACATGTATCGATACA
1539954 TCTGGGTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACCAAGCAACATGTATCGATACAA
Found at i:1540074 original size:20 final size:21
Alignment explanation
Indices: 1540049--1540092 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
1540039 GATACTTTGA
*
1540049 ATTATTTTTA-CTTGAAAAAC
1 ATTATTTTTAGCTTAAAAAAC
1540069 ATTATTTTTATGCTTAAAAAAC
1 ATTATTTTTA-GCTTAAAAAAC
1540091 AT
1 AT
1540093 CTATACTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
22 11 0.52
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
ATTATTTTTAGCTTAAAAAAC
Found at i:1544855 original size:34 final size:33
Alignment explanation
Indices: 1544812--1544948 Score: 93
Period size: 36 Copynumber: 4.0 Consensus size: 33
1544802 GATAGAAACC
1544812 TCCCTATCTTTTCATGACCTAAGATAAAACCTCT
1 TCCCTATCTTTTCA-GACCTAAGATAAAACCTCT
* *
1544846 TCCCTATCTTTTTCAAAGGCTAAGATAGAAA-C-CT
1 TCCCTATC-TTTTCAGA-CCTAAGATA-AAACCTCT
* *
1544880 T-CCTATCTTTTCACGGGCC-AAGATAGAACCTCT
1 TCCCTATCTTTTCA--GACCTAAGATAAAACCTCT
* * * *
1544913 CTGCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 -TCCCTATC-TTTTCAGA-CCTAAGATAAAACCTCT
1544949 CAATCATTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
31 2 0.02
32 13 0.16
33 9 0.11
34 13 0.16
35 22 0.27
36 23 0.28
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (33 bp):
TCCCTATCTTTTCAGACCTAAGATAAAACCTCT
Found at i:1544876 original size:67 final size:68
Alignment explanation
Indices: 1544790--1544947 Score: 234
Period size: 67 Copynumber: 2.4 Consensus size: 68
1544780 CAACATTATC
*
1544790 TTTC-AAGGCTAAGATAGAAACCTCCCTATCTTTTCA-TGACCTAAGATAAAACCTCT-TCCCTA
1 TTTCAAAGGCTAAGATAGAAACCTCCCTATCTTTTCACGGACC-AAGATAAAACCTCTCTCCCTA
1544852 TCTT
65 TCTT
* * * *
1544856 TTTCAAAGGCTAAGATAGAAACCTTCCTATCTTTTCACGGGCCAAGATAGAACCTCTCTGCCTAT
1 TTTCAAAGGCTAAGATAGAAACCTCCCTATCTTTTCACGGACCAAGATAAAACCTCTCTCCCTAT
1544921 CTT
66 CTT
1544924 TTTCAAAGGCTAAGATAG-AACCTC
1 TTTCAAAGGCTAAGATAGAAACCTC
1544948 TCAATCATTT
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
66 4 0.05
67 49 0.59
68 30 0.36
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (68 bp):
TTTCAAAGGCTAAGATAGAAACCTCCCTATCTTTTCACGGACCAAGATAAAACCTCTCTCCCTAT
CTT
Found at i:1544939 original size:36 final size:34
Alignment explanation
Indices: 1544786--1544949 Score: 155
Period size: 32 Copynumber: 4.9 Consensus size: 34
1544776 CTTACAACAT
*
1544786 TATC-TTTC-AAGGCTAAGATAGAAAC-CTC-CC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
* * *
1544816 TATCTTTTC-ATGACCTAAGATAAAACCTCT-TCCC
1 TATCTTTTCAAAG-GCTAAGATAGAACCTCTCT-CC
*
1544850 TATCTTTTTCAAAGGCTAAGATAGAAAC-CT-TCC
1 TATC-TTTTCAAAGGCTAAGATAGAACCTCTCTCC
** *
1544883 TATCTTTTCACGGGCCAAGATAGAACCTCTCTGCC
1 TATCTTTTCAAAGGCTAAGATAGAACCTCTCT-CC
1544918 TATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 TATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1544950 AATCATTTAG
Statistics
Matches: 108, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
30 4 0.04
31 6 0.06
32 30 0.28
33 10 0.09
34 10 0.09
35 22 0.20
36 26 0.24
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (34 bp):
TATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
Found at i:1545402 original size:20 final size:20
Alignment explanation
Indices: 1545377--1545430 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1545367 ATTGGGCTCA
1545377 ATGTATC-AGTACAATTCACC
1 ATGTATCGA-TACAATTCACC
*
1545397 ATGTATCGATACAATTCATC
1 ATGTATCGATACAATTCACC
1545417 ATGTATCGATACAA
1 ATGTATCGATACAA
1545431 AATGAGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:1545642 original size:19 final size:20
Alignment explanation
Indices: 1545618--1545656 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
1545608 GATACTTTAA
1545618 ATTATTTTTA-CTTGAAAAC
1 ATTATTTTTAGCTTGAAAAC
1545637 ATTATTTTTATGCTTGAAAA
1 ATTATTTTTA-GCTTGAAAA
1545657 ACATCTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (20 bp):
ATTATTTTTAGCTTGAAAAC
Found at i:1546351 original size:33 final size:33
Alignment explanation
Indices: 1546308--1546377 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
1546298 GTTTTCTTTT
*
1546308 ATGGACAAATTTTCAGGCTACAATAAGATTAAA
1 ATGGACAAATTTTCAAGCTACAATAAGATTAAA
* *
1546341 ATGGATAAATTTTCAAGCTACAATCAGATTAAA
1 ATGGACAAATTTTCAAGCTACAATAAGATTAAA
1546374 ATGG
1 ATGG
1546378 CTTCAGAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (33 bp):
ATGGACAAATTTTCAAGCTACAATAAGATTAAA
Found at i:1549382 original size:11 final size:11
Alignment explanation
Indices: 1549368--1549397 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
1549358 GTTCAGCTAA
1549368 AAAAAAGAGAG
1 AAAAAAGAGAG
1549379 AAAAAAGAGAG
1 AAAAAAGAGAG
1549390 AAAGAAAG
1 AAA-AAAG
1549398 GTAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.78
12 4 0.22
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (11 bp):
AAAAAAGAGAG
Found at i:1549406 original size:23 final size:22
Alignment explanation
Indices: 1549380--1549429 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
1549370 AAAAGAGAGA
1549380 AAAAAGAGA-GAAAGAAAGGTAAG
1 AAAAAGAGAGGAAA-AAAGGT-AG
* *
1549403 AAAAATAGAGGAAAATAGGTAG
1 AAAAAGAGAGGAAAAAAGGTAG
1549425 AAAAA
1 AAAAA
1549430 TAGAAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 13 0.54
24 4 0.17
ACGTcount: A:0.66, C:0.00, G:0.26, T:0.08
Consensus pattern (22 bp):
AAAAAGAGAGGAAAAAAGGTAG
Found at i:1549426 original size:22 final size:25
Alignment explanation
Indices: 1549377--1549433 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 25
1549367 AAAAAAAGAG
1549377 AGAAAAA-AGAGAGAAAGAAAGGTA
1 AGAAAAATAGAGAGAAAGAAAGGTA
*
1549401 AGAAAAATAGAG-GAAA-ATAGGT-
1 AGAAAAATAGAGAGAAAGAAAGGTA
1549423 AGAAAAATAGA
1 AGAAAAATAGA
1549434 AAACTAAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 11 0.35
23 5 0.16
24 11 0.35
25 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (25 bp):
AGAAAAATAGAGAGAAAGAAAGGTA
Found at i:1550838 original size:154 final size:153
Alignment explanation
Indices: 1550640--1551020 Score: 498
Period size: 154 Copynumber: 2.5 Consensus size: 153
1550630 CTTTTATCAT
* * **
1550640 CCTTTTTAAGT-CTTTAAAGGTATCGAGTACTTCTACGTCAAAGGTATTTCCTAGGGACATTTTC
1 CCTTTTTAAGTCCTTTAAGGGTATCGAGTACTTCTACGTCGAAGGTATACCCTAGGG-CATTTTC
* ** * *
1550704 ATAATTTTCTAAAACCAACTCCTAGGTTGTTA-CTGAGTCTGCTTTTATGCCAAAGGTGGGCATT
65 ATAATTTTCCAAAACCAACTCCTAGGTCATCATC-GAGTATGCTTTTATGCCAAAGGTGGGCATT
*
1550768 TAGGATAGGTTCATTCCATCTTAAA
129 TAGGATAGGTTCATCCCATCTTAAA
* * * *
1550793 CCTTTTTAAGTCCTTTAGGGGTATCGGGTACTTCTACGTCGAAGGTATCCCCTAGGGGCATTTTT
1 CCTTTTTAAGTCCTTTAAGGGTATCGAGTACTTCTACGTCGAAGGTATACCCTA-GGGCATTTTC
* *
1550858 GTAATTTTCCAAAACCAACTCGTAGGTCATCATCGAGTATGCTTTTATGCCAAAGGTGGGCATTT
65 ATAATTTTCCAAAACCAACTCCTAGGTCATCATCGAGTATGCTTTTATGCCAAAGGTGGGCATTT
*
1550923 ATGATAGGTTCATCCCATCTTAAA
130 AGGATAGGTTCATCCCATCTTAAA
* * *
1550947 CCTTTTTTTAAGTCC-TTAAGGGAATCGAGTACTTCTACGTCGACGGCATACCCTAAGGGCATTT
1 CC--TTTTTAAGTCCTTTAAGGGTATCGAGTACTTCTACGTCGAAGGTATACCCT-AGGGCATTT
*
1551011 TCTTAATTTT
63 TCATAATTTT
1551021 TCTATGAAAC
Statistics
Matches: 198, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
153 11 0.06
154 122 0.62
155 53 0.27
156 12 0.06
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (153 bp):
CCTTTTTAAGTCCTTTAAGGGTATCGAGTACTTCTACGTCGAAGGTATACCCTAGGGCATTTTCA
TAATTTTCCAAAACCAACTCCTAGGTCATCATCGAGTATGCTTTTATGCCAAAGGTGGGCATTTA
GGATAGGTTCATCCCATCTTAAA
Found at i:1552035 original size:13 final size:13
Alignment explanation
Indices: 1552017--1552042 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1552007 TACACCAAGT
1552017 ATGTATCGATACA
1 ATGTATCGATACA
1552030 ATGTATCGATACA
1 ATGTATCGATACA
1552043 CCAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1556143 original size:15 final size:15
Alignment explanation
Indices: 1556125--1556154 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1556115 CCAAATTGAG
1556125 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
1556140 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
1556155 ATTGATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:1556150 original size:16 final size:16
Alignment explanation
Indices: 1556114--1556154 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
1556104 GAGACAAATG
* *
1556114 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
1556130 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
1556145 TCC-AAATGAA
1 TCCAAAATGAA
1556155 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:1558393 original size:20 final size:20
Alignment explanation
Indices: 1558355--1558394 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
1558345 TTTTGCGAAA
1558355 TACTTGTTTTTCACTTCAAAT
1 TACTTGTTTTTCAC-TCAAAT
1558376 TACTTCGTTTTTCA-TCAAA
1 TACTT-GTTTTTCACTCAAA
1558395 AGCAGCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TACTTGTTTTTCACTCAAAT
Found at i:1564334 original size:45 final size:46
Alignment explanation
Indices: 1564284--1564944 Score: 271
Period size: 46 Copynumber: 14.7 Consensus size: 46
1564274 TTCATCTCTG
*
1564284 TTTGACGTGATGG-TTTAGGCCTGGTCAAA-TTTCTTATATATTTCA
1 TTTGACGTGATGGTTTTAGCCCTGGTCAAACTTTCTT-TATATTTCA
* * * *
1564329 TTTGACGTGATGGTTTTTGCCCTGGTTAAAC--TCATTT-TCTTTCTTT
1 TTTGACGTGATGGTTTTAGCCCTGGTCAAACTTTC-TTTATATTTC--A
* *
1564375 TTTGACGTGATGGTTTTCGCCTTGGTCAAACTTTCTTTATATTTCA
1 TTTGACGTGATGGTTTTAGCCCTGGTCAAACTTTCTTTATATTTCA
* ** *
1564421 TTTGACATGATGGTTCTTA-CTTTGGTCAAACTTCCTTTATATTTC-
1 TTTGACGTGATGGTT-TTAGCCCTGGTCAAACTTTCTTTATATTTCA
* * * * *
1564466 GTTGACGTGATGGTTTTCGCCCTGGTCAAACTCTT-TTGACATTTTTA
1 TTTGACGTGATGGTTTTAGCCCTGGTCAAACT-TTCTTTATA-TTTCA
* * * *
1564513 TTTGATGTGATGGTTTTCA-TCCTGGTCAAACTTCCTTTATATTTCG
1 TTTGACGTGATGGTTTT-AGCCCTGGTCAAACTTTCTTTATATTTCA
* ** * * * *
1564559 TTTAATATAATGGTTCTT-GCCCTAGTCAAAC-TCCTTTGATATCTCTA
1 TTTGACGTGATGGTT-TTAGCCCTGGTCAAACTTTCTTT-ATATTTC-A
** * * * *
1564606 TTTGAAATGATGGTGTT-CCACCTAGTCAAAC--TC-----CTTTCA
1 TTTGACGTGATGGTTTTAGC-CCTGGTCAAACTTTCTTTATATTTCA
* * ** * * * *
1564645 -CTGATGTGATGGTTTTTTCTCTGGTCAAAC--TATTT-TCTTTCT
1 TTTGACGTGATGGTTTTAGCCCTGGTCAAACTTTCTTTATATTTCA
*
1564687 TGCTTGATGTGATGG-TTTAGCCCTGGTCAAAC--TCTTTATATTTCA
1 T--TTGACGTGATGGTTTTAGCCCTGGTCAAACTTTCTTTATATTTCA
* * * * *
1564732 TTTGACGTGATGGTTCTCA-CCTTGATCAAACTCTT-TTAATACTTT-G
1 TTTGACGTGATGGTT-TTAGCCCTGGTCAAACT-TTCTTTATA-TTTCA
* * * * * *
1564778 TTTGACGTGATGG-TCTCGCCTTAGTCAAAC-TCCTTTGATATTTTA
1 TTTGACGTGATGGTTTTAGCCCTGGTCAAACTTTCTTT-ATATTTCA
** * * *
1564823 TTTGACACGATGGCTTTT-GCCCTAGTCAAATTCTTCTTCT-T-TCTCA
1 TTTGACGTGATGG-TTTTAGCCCTGGTCAAACT-TTCTT-TATATTTCA
* * **
1564869 TTTGATGTGATGGTTTTA-CCTTGGTCAAA--TTCTTTATATTTTG
1 TTTGACGTGATGGTTTTAGCCCTGGTCAAACTTTCTTTATATTTCA
* * ** *
1564912 TTTAATGTGATGGTCCTAGCCTTGGTCAAACTT
1 TTTGACGTGATGGTTTTAGCCCTGGTCAAACTT
1564945 GTTACATCTA
Statistics
Matches: 470, Mismatches: 96, Indels: 99
0.71 0.14 0.15
Matches are distributed among these distances:
38 22 0.05
39 2 0.00
40 3 0.01
41 1 0.00
42 11 0.02
43 29 0.06
44 52 0.11
45 107 0.23
46 164 0.35
47 67 0.14
48 11 0.02
49 1 0.00
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.45
Consensus pattern (46 bp):
TTTGACGTGATGGTTTTAGCCCTGGTCAAACTTTCTTTATATTTCA
Found at i:1564545 original size:138 final size:138
Alignment explanation
Indices: 1564305--1564576 Score: 356
Period size: 138 Copynumber: 2.0 Consensus size: 138
1564295 GGTTTAGGCC
* * * *
1564305 TGGTCAAATTTCTTATATATTTCATTTGACGTGATGGTTTTTGCCCTGGTTAAACTCATTTTCTT
1 TGGTCAAATTCCTTATATATTTCAGTTGACGTGATGGTTTTCGCCCTGGTCAAACTCATTTTCTT
* * * *
1564370 TCTTTTTTGACGTGATGGTTTTCGCCTTGGTCAAACTTTCTTTATATTTCATTTGACATGATGGT
66 TCTTATTTGACGTGATGGTTTTCGCCTTGGTCAAACTTCCTTTATATTTCATTTAACATAATGGT
1564435 TCTTACTT
131 TCTTACTT
1564443 TGGTCAAACTTCCTT-TATATTTC-GTTGACGTGATGGTTTTCGCCCTGGTCAAACTC-TTTTGA
1 TGGTCAAA-TTCCTTATATATTTCAGTTGACGTGATGGTTTTCGCCCTGGTCAAACTCATTTT--
* * * *
1564505 CATTT-TTATTTGATGTGATGGTTTTCATCC-TGGTCAAACTTCCTTTATATTTCGTTTAATATA
63 C-TTTCTTATTTGACGTGATGGTTTTC-GCCTTGGTCAAACTTCCTTTATATTTCATTTAACATA
1564568 ATGGTTCTT
126 ATGGTTCTT
1564577 GCCCTAGTCA
Statistics
Matches: 117, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
136 4 0.03
137 30 0.26
138 73 0.62
139 10 0.09
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.49
Consensus pattern (138 bp):
TGGTCAAATTCCTTATATATTTCAGTTGACGTGATGGTTTTCGCCCTGGTCAAACTCATTTTCTT
TCTTATTTGACGTGATGGTTTTCGCCTTGGTCAAACTTCCTTTATATTTCATTTAACATAATGGT
TCTTACTT
Found at i:1564617 original size:93 final size:92
Alignment explanation
Indices: 1564443--1564642 Score: 235
Period size: 93 Copynumber: 2.2 Consensus size: 92
1564433 GTTCTTACTT
* * * * *
1564443 TGGTCAAACTTCCTTTATATTTCGTTGACGTGATGGTTTTCGCCCTGGTCAAACTCTTTTGACAT
1 TGGTCAAACTTCCTTTATATTTCGTTAACATAATGGTTTTCGCCCTAGTCAAACTCCTTTGACAT
* * ** *
1564508 TTTTATTTGATGTGATGGT-TTTCATCC
66 CTCTATTTGAAATGATGGTGTTCCA-CC
* *
1564535 TGGTCAAACTTCCTTTATATTTCGTTTAATATAATGGTTCTT-GCCCTAGTCAAACTCCTTTGAT
1 TGGTCAAACTTCCTTTATATTTCG-TTAACATAATGGTT-TTCGCCCTAGTCAAACTCCTTTGAC
1564599 ATCTCTATTTGAAATGATGGTGTTCCACC
64 ATCTCTATTTGAAATGATGGTGTTCCACC
*
1564628 TAGTCAAAC-TCCTTT
1 TGGTCAAACTTCCTTT
1564643 CACTGATGTG
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
92 30 0.33
93 56 0.61
94 6 0.07
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.43
Consensus pattern (92 bp):
TGGTCAAACTTCCTTTATATTTCGTTAACATAATGGTTTTCGCCCTAGTCAAACTCCTTTGACAT
CTCTATTTGAAATGATGGTGTTCCACC
Found at i:1566885 original size:17 final size:16
Alignment explanation
Indices: 1566865--1566896 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1566855 CATGAAAATT
1566865 GAAAAATAAAGAAAAAA
1 GAAAAATAAA-AAAAAA
1566882 GAAAAATAAAAAAAA
1 GAAAAATAAAAAAAA
1566897 TAAAGTTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (16 bp):
GAAAAATAAAAAAAAA
Found at i:1567094 original size:12 final size:12
Alignment explanation
Indices: 1567077--1567110 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1567067 TCTTATTTTA
1567077 CTTTCTTTCTTG
1 CTTTCTTTCTTG
1567089 CTTTCTTTCTTG
1 CTTTCTTTCTTG
*
1567101 -TTTATTTCTT
1 CTTTCTTTCTT
1567111 CATGATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.03, C:0.21, G:0.06, T:0.71
Consensus pattern (12 bp):
CTTTCTTTCTTG
Found at i:1569772 original size:13 final size:13
Alignment explanation
Indices: 1569754--1569778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1569744 ACATTATGCT
1569754 TTGTATCGATACA
1 TTGTATCGATACA
1569767 TTGTATCGATAC
1 TTGTATCGATAC
1569779 GTGATCATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1569810 original size:20 final size:19
Alignment explanation
Indices: 1569765--1569821 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
1569755 TGTATCGATA
*
1569765 CATTGTATCGATACGTGAT
1 CATTGTATCGATACATGAT
1569784 CATTGTATCGATACATGCA-
1 CATTGTATCGATACATG-AT
1569803 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
1569822 AGCTGGCAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
19 18 0.51
20 17 0.49
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:1569874 original size:20 final size:20
Alignment explanation
Indices: 1569849--1569902 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1569839 CTACCACTGT
1569849 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAGCA-A
*
1569869 TTGTATCGATACATGAGGAA
1 TTGTATCGATACATGAGCAA
1569889 TTGTATCGATACAT
1 TTGTATCGATACAT
1569903 TGTCCCAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (20 bp):
TTGTATCGATACATGAGCAA
Found at i:1570512 original size:186 final size:186
Alignment explanation
Indices: 1570198--1570573 Score: 752
Period size: 186 Copynumber: 2.0 Consensus size: 186
1570188 TTAATCTTTG
1570198 AAAGCTCTTTGTATTTGATTTGTGTTTACTCTTTCACAAACATCAGTCTATTTAGAGGTTATTTT
1 AAAGCTCTTTGTATTTGATTTGTGTTTACTCTTTCACAAACATCAGTCTATTTAGAGGTTATTTT
1570263 TGTTTGTATAATTACCTTGAATTGTATAAGGTTGCATTCAACCTTGGGTTACAATTTCTCAAGAA
66 TGTTTGTATAATTACCTTGAATTGTATAAGGTTGCATTCAACCTTGGGTTACAATTTCTCAAGAA
1570328 TTGGGAATATAATTCTTGAAGAGATTGTGAGGTGTTTATCTTAGCCTAGAAAAGAT
131 TTGGGAATATAATTCTTGAAGAGATTGTGAGGTGTTTATCTTAGCCTAGAAAAGAT
1570384 AAAGCTCTTTGTATTTGATTTGTGTTTACTCTTTCACAAACATCAGTCTATTTAGAGGTTATTTT
1 AAAGCTCTTTGTATTTGATTTGTGTTTACTCTTTCACAAACATCAGTCTATTTAGAGGTTATTTT
1570449 TGTTTGTATAATTACCTTGAATTGTATAAGGTTGCATTCAACCTTGGGTTACAATTTCTCAAGAA
66 TGTTTGTATAATTACCTTGAATTGTATAAGGTTGCATTCAACCTTGGGTTACAATTTCTCAAGAA
1570514 TTGGGAATATAATTCTTGAAGAGATTGTGAGGTGTTTATCTTAGCCTAGAAAAGAT
131 TTGGGAATATAATTCTTGAAGAGATTGTGAGGTGTTTATCTTAGCCTAGAAAAGAT
1570570 AAAG
1 AAAG
1570574 TGTTGTAAGG
Statistics
Matches: 190, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
186 190 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (186 bp):
AAAGCTCTTTGTATTTGATTTGTGTTTACTCTTTCACAAACATCAGTCTATTTAGAGGTTATTTT
TGTTTGTATAATTACCTTGAATTGTATAAGGTTGCATTCAACCTTGGGTTACAATTTCTCAAGAA
TTGGGAATATAATTCTTGAAGAGATTGTGAGGTGTTTATCTTAGCCTAGAAAAGAT
Found at i:1577143 original size:20 final size:19
Alignment explanation
Indices: 1577120--1577237 Score: 80
Period size: 20 Copynumber: 6.7 Consensus size: 19
1577110 CACATCCAAA
1577120 TGTATCGATACATTATGCTT
1 TGTATCGATACATTAT-CTT
1577140 TGTATCGATAC---A---T
1 TGTATCGATACATTATCTT
*
1577153 TGTATCGATGCATTATGCTT
1 TGTATCGATACATTAT-CTT
1577173 TGTATCGATAC---A---T
1 TGTATCGATACATTATCTT
*
1577186 TGTATCGTTACATTATGCTT
1 TGTATCGATACATTAT-CTT
* * *
1577206 TGTATTGATACATGATCAT
1 TGTATCGATACATTATCTT
1577225 TGTATCGATACAT
1 TGTATCGATACAT
1577238 GCACAATTGT
Statistics
Matches: 76, Mismatches: 8, Indels: 29
0.67 0.07 0.26
Matches are distributed among these distances:
13 22 0.29
16 2 0.03
17 2 0.03
19 14 0.18
20 36 0.47
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATTATCTT
Found at i:1577157 original size:13 final size:13
Alignment explanation
Indices: 1577139--1577199 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 13
1577129 ACATTATGCT
1577139 TTGTATCGATACA
1 TTGTATCGATACA
*
1577152 TTGTATCGATGCA
1 TTGTATCGATACA
*
1577165 -T-TAT-G---CT
1 TTGTATCGATACA
1577172 TTGTATCGATACA
1 TTGTATCGATACA
*
1577185 TTGTATCGTTACA
1 TTGTATCGATACA
1577198 TT
1 TT
1577200 ATGCTTTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.08
10 2 0.05
11 3 0.08
12 1 0.03
13 27 0.71
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1577167 original size:33 final size:33
Alignment explanation
Indices: 1577120--1577218 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
1577110 CACATCCAAA
1577120 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCTTTGTATCGATACAT
*
1577153 TGTATCGATGCATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCTTTGTATCGATACAT
* *
1577186 TGTATCGTTACATTATGCTTTGTATTGATACAT
1 TGTATCGATACATTATGCTTTGTATCGATACAT
1577219 GATCATTGTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACATTATGCTTTGTATCGATACAT
Found at i:1577248 original size:20 final size:19
Alignment explanation
Indices: 1577183--1577259 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
1577173 TGTATCGATA
* *
1577183 CATTGTATCGTTACATTAT
1 CATTGTATCGATACATGAT
* *
1577202 GCTTTGTATTGATACATGAT
1 -CATTGTATCGATACATGAT
1577222 CATTGTATCGATACATGCA-
1 CATTGTATCGATACATG-AT
1577241 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
1577260 AACTGACAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 17 0.35
20 32 0.65
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:1577312 original size:20 final size:20
Alignment explanation
Indices: 1577287--1577340 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1577277 TTACCACTGT
*
1577287 TTGTATCGATACATG-GCATA
1 TTGTATTGATACATGAGCA-A
*
1577307 TTGTATTGATACATGAGGAA
1 TTGTATTGATACATGAGCAA
1577327 TTGTATTGATACAT
1 TTGTATTGATACAT
1577341 TGTCCCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGTATTGATACATGAGCAA
Found at i:1579743 original size:15 final size:16
Alignment explanation
Indices: 1579723--1579765 Score: 70
Period size: 15 Copynumber: 2.7 Consensus size: 16
1579713 CATTCAAACA
1579723 TTTTTTCTAAAGG-AT
1 TTTTTTCTAAAGGAAT
1579738 TTTTTTCTAAAGGACAT
1 TTTTTTCTAAAGGA-AT
1579755 TTTTTTCTAAA
1 TTTTTTCTAAA
1579766 TAATTTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 13 0.50
17 13 0.50
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (16 bp):
TTTTTTCTAAAGGAAT
Found at i:1579771 original size:15 final size:15
Alignment explanation
Indices: 1579723--1579771 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
1579713 CATTCAAACA
*
1579723 TTTTTTCTAAAGGAT
1 TTTTTTCTAAAGAAT
1579738 TTTTTTCTAAAGGACAT
1 TTTTTTCTAAA-GA-AT
*
1579755 TTTTTTCTAAATAAT
1 TTTTTTCTAAAGAAT
1579770 TT
1 TT
1579772 CTTCCAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 15 0.50
16 2 0.07
17 13 0.43
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (15 bp):
TTTTTTCTAAAGAAT
Found at i:1585635 original size:20 final size:20
Alignment explanation
Indices: 1585610--1585699 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
1585600 ACCCTAAAAA
*
1585610 GTATCGATACACATTTAATT
1 GTATCGATACACATTGAATT
** *
1585630 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
*
1585650 GTATCGATACACATTTAATT
1 GTATCGATACACATTGAATT
** *
1585670 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
1585690 GTATCGATAC
1 GTATCGATAC
1585700 TTGAAAAAGA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:1585665 original size:40 final size:40
Alignment explanation
Indices: 1585610--1585699 Score: 180
Period size: 40 Copynumber: 2.2 Consensus size: 40
1585600 ACCCTAAAAA
1585610 GTATCGATACACATTTAATTGTATCGATACATGTTGCATT
1 GTATCGATACACATTTAATTGTATCGATACATGTTGCATT
1585650 GTATCGATACACATTTAATTGTATCGATACATGTTGCATT
1 GTATCGATACACATTTAATTGTATCGATACATGTTGCATT
1585690 GTATCGATAC
1 GTATCGATAC
1585700 TTGAAAAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (40 bp):
GTATCGATACACATTTAATTGTATCGATACATGTTGCATT
Found at i:1585791 original size:13 final size:13
Alignment explanation
Indices: 1585773--1585797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1585763 ACACATAGTA
1585773 TGTATCGATACAT
1 TGTATCGATACAT
1585786 TGTATCGATACA
1 TGTATCGATACA
1585798 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1585794 original size:32 final size:33
Alignment explanation
Indices: 1585753--1585820 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
1585743 GTAGCTAAAC
**
1585753 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1585785 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1585818 TTG
1 TTG
1585821 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:1591982 original size:13 final size:13
Alignment explanation
Indices: 1591964--1592002 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1591954 ACAGAATTCT
1591964 TTGTATCGATACA
1 TTGTATCGATACA
1591977 TTGTATCGATACA
1 TTGTATCGATACA
*
1591990 CTGTATCGATACA
1 TTGTATCGATACA
1592003 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1594417 original size:20 final size:20
Alignment explanation
Indices: 1594392--1594441 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1594382 ACCCTGAAAA
*
1594392 GTATCGATACACATTTAATT
1 GTATCGATACACATTGAATT
** *
1594412 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
1594432 GTATCGATAC
1 GTATCGATAC
1594442 TTGAAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:1594533 original size:13 final size:13
Alignment explanation
Indices: 1594515--1594539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1594505 ACACATAGTA
1594515 TGTATCGATACAT
1 TGTATCGATACAT
1594528 TGTATCGATACA
1 TGTATCGATACA
1594540 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1594536 original size:32 final size:33
Alignment explanation
Indices: 1594495--1594562 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1594485 GTAGCTAAAC
**
1594495 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
*
1594527 TTGTATCGATACACCATAAAATGTATTGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
1594560 TTG
1 TTG
1594563 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:1595470 original size:16 final size:17
Alignment explanation
Indices: 1595438--1595470 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1595428 GATAATATGA
*
1595438 TTTATTATCTATTACTT
1 TTTATTACCTATTACTT
1595455 TTTATTACCT-TTACTT
1 TTTATTACCTATTACTT
1595471 ATATATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTATTACCTATTACTT
Found at i:1596609 original size:22 final size:23
Alignment explanation
Indices: 1596566--1596608 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
1596556 TTTATGTCAA
1596566 AAAAGAAATTAATAAAATAAAAT
1 AAAAGAAATTAATAAAATAAAAT
*
1596589 AAAAG-AATTAA-AAATTAAAA
1 AAAAGAAATTAATAAAATAAAA
1596609 ATGAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (23 bp):
AAAAGAAATTAATAAAATAAAAT
Found at i:1598006 original size:20 final size:20
Alignment explanation
Indices: 1597978--1598029 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1597968 GGGCTTAATA
*
1597978 TATCGATACATTTTACCATG
1 TATCGATACATTTCACCATG
* * *
1597998 TATCAATACAATTCATCATG
1 TATCGATACATTTCACCATG
1598018 TATCGATACATT
1 TATCGATACATT
1598030 GTATCGATAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (20 bp):
TATCGATACATTTCACCATG
Found at i:1602248 original size:13 final size:13
Alignment explanation
Indices: 1602230--1602256 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1602220 ATACTTGTAC
1602230 TATCAAAATATCT
1 TATCAAAATATCT
1602243 TATCAAAATATCT
1 TATCAAAATATCT
1602256 T
1 T
1602257 TTCCTTTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TATCAAAATATCT
Found at i:1607106 original size:13 final size:13
Alignment explanation
Indices: 1607088--1607112 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1607078 TACTATGAAC
1607088 ATGTATCGATACG
1 ATGTATCGATACG
1607101 ATGTATCGATAC
1 ATGTATCGATAC
1607113 TAAGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACG
Found at i:1609067 original size:13 final size:13
Alignment explanation
Indices: 1609049--1609073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1609039 TGATTCTTAA
1609049 TGTATCGATACAT
1 TGTATCGATACAT
1609062 TGTATCGATACA
1 TGTATCGATACA
1609074 AACAGTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1613934 original size:17 final size:18
Alignment explanation
Indices: 1613898--1613935 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1613888 TAGCTAAACT
1613898 TGTATCGATACACATAGTA
1 TGTATCGATA-ACATAGTA
*
1613917 TGTATCGAT-ACATTGTA
1 TGTATCGATAACATAGTA
1613934 TG
1 TG
1613936 GATACACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (18 bp):
TGTATCGATAACATAGTA
Found at i:1613958 original size:33 final size:32
Alignment explanation
Indices: 1613897--1613964 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1613887 GTAGCTAAAC
**
1613897 TTGTATCGATACACATAGTATGTATCGATACA
1 TTGTATCGATACACATAAAATGTATCGATACA
*
1613929 TTGTATGGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACA-CATAAAATGTATCGATACA
1613962 TTG
1 TTG
1613965 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACATAAAATGTATCGATACA
Found at i:1615567 original size:9 final size:9
Alignment explanation
Indices: 1615553--1615582 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1615543 ATCAAGGATC
1615553 ATGAAGATG
1 ATGAAGATG
1615562 ATGAAGATG
1 ATGAAGATG
*
1615571 ATGATGATG
1 ATGAAGATG
1615580 ATG
1 ATG
1615583 GTGACTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (9 bp):
ATGAAGATG
Found at i:1622593 original size:20 final size:20
Alignment explanation
Indices: 1622568--1622617 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1622558 ACCCTGAAAA
*
1622568 GTATCGATACACATTTAATT
1 GTATCGATACACATTGAATT
** *
1622588 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
1622608 GTATCGATAC
1 GTATCGATAC
1622618 TTGAAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:1622708 original size:17 final size:18
Alignment explanation
Indices: 1622672--1622709 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1622662 TAGCTAAACT
1622672 TGTATCGATACACATAGTA
1 TGTATCGATA-ACATAGTA
*
1622691 TGTATCGAT-ACATTGTA
1 TGTATCGATAACATAGTA
1622708 TG
1 TG
1622710 GATACACCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (18 bp):
TGTATCGATAACATAGTA
Found at i:1622732 original size:33 final size:32
Alignment explanation
Indices: 1622671--1622738 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
1622661 GTAGCTAAAC
**
1622671 TTGTATCGATACACATAGTATGTATCGATACA
1 TTGTATCGATACACATAAAATGTATCGATACA
*
1622703 TTGTATGGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACA-CATAAAATGTATCGATACA
1622736 TTG
1 TTG
1622739 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACATAAAATGTATCGATACA
Found at i:1623851 original size:19 final size:19
Alignment explanation
Indices: 1623806--1623862 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1623796 ACTGCCAGTT
* *
1623806 TCATGTATCAATACAATTGC
1 TCATGTATCGATACAA-TGA
*
1623826 GCATGTATCGATACAATGA
1 TCATGTATCGATACAATGA
1623845 TCATGTATCGATACAATG
1 TCATGTATCGATACAATG
1623863 TATCGATACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 19 0.58
20 14 0.42
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:1623865 original size:13 final size:13
Alignment explanation
Indices: 1623847--1623873 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1623837 TACAATGATC
1623847 ATGTATCGATACA
1 ATGTATCGATACA
1623860 ATGTATCGATACA
1 ATGTATCGATACA
1623873 A
1 A
1623874 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1623869 original size:32 final size:33
Alignment explanation
Indices: 1623828--1623890 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
1623818 ACAATTGCGC
* *
1623828 ATGTATCGATACAATG-ATCATGTATCGATACA
1 ATGTATCGATACAAAGCATAATGTATCGATACA
1623860 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
1623891 TATCTGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATACA
Found at i:1628664 original size:13 final size:13
Alignment explanation
Indices: 1628646--1628671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1628636 TAATAAGTGT
1628646 TGTATCGATACAA
1 TGTATCGATACAA
1628659 TGTATCGATACAA
1 TGTATCGATACAA
1628672 AAGCTACCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1632828 original size:30 final size:30
Alignment explanation
Indices: 1632785--1632854 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
1632775 ATTTTATTTA
*
1632785 AGCTTGCACAATTAATTAGGTTTGGATTATT
1 AGCTAGCA-AATTAATTAGGTTTGGATTATT
1632816 AGCTAGCAAATTAATTAGGTTTGGATTATT
1 AGCTAGCAAATTAATTAGGTTTGGATTATT
1632846 AGCTAGCAA
1 AGCTAGCAA
1632855 GCTAATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 31 0.82
31 7 0.18
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (30 bp):
AGCTAGCAAATTAATTAGGTTTGGATTATT
Found at i:1638103 original size:49 final size:50
Alignment explanation
Indices: 1637925--1638380 Score: 461
Period size: 52 Copynumber: 9.0 Consensus size: 50
1637915 GAAGAGTGAT
* * *
1637925 AAAGGTGCCAATATGCTGATTC-AGGACTAGCGATATTGGGCTTAAAGATG
1 AAAGGTGCCAATATGCTGATTCAAGG-CCAGCGACATTGGACTTAAAGATG
** * * * ** * * * *
1637975 TAAAAAATGTCAATGTGCTGATTCACGATCGGCAACATTAGACTTGAAGATG
1 --AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * ** *
1638027 AGAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGTTTAAAGGTG
1 A-AAG-GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * *
1638079 -AAGGTGCTAATGTGCTGATTCAAGGGCAGTGACATTGGACTTAAAGATG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* *
1638128 ACAAAGGTGCAAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 --AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * *
1638180 -AAGGTGCCAATGTGCTAATTCAAGGCCAGCAACATTGGACTTAAAGGTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
*
1638229 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 --AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * *
1638281 -AAGGTGTCAATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* *
1638330 ACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 --AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
1638381 AGATGCAACC
Statistics
Matches: 333, Mismatches: 58, Indels: 25
0.80 0.14 0.06
Matches are distributed among these distances:
49 127 0.38
50 4 0.01
51 2 0.01
52 196 0.59
53 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.24
Consensus pattern (50 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
Found at i:1638147 original size:101 final size:101
Alignment explanation
Indices: 1637920--1638380 Score: 561
Period size: 101 Copynumber: 4.5 Consensus size: 101
1637910 GATGAGAAGA
* * * **
1637920 GTGATAAAGGTGCCAATATGCTGATTC-AGGACTAGCGATATTGGGCTTAAAGATGTAAAAAATG
1 GTGACAAAGGTGCCAATATGCTGATTCAAGG-CCAGCGATATTGGACTTAAAGATG---AAGGTG
* ** * * *
1637984 -TCAATGTGCTGATTCACGATCGGCAACATTAGACTTGAAG
62 CT-AATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* * * * * ** *
1638024 ATGA-GAAGAATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGTTTAAAGGTGAAGGTGCTA
1 GTGACAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCTA
* **
1638088 ATGTGCTGATTCAAGGGCAGTGACATTGGACTTAAAG
65 ATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
* * *
1638125 ATGACAAAGGTGCAAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAA
1 GTGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCTAA
*
1638190 TGTGCTAATTCAAGGCCAGCAACATTGGACTTAAAG
66 TGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
*
1638226 GTGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTG-TCA
1 GTGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCT-A
*
1638290 ATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
65 ATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
*
1638327 GTGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 GTGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
1638381 AGATGCAACC
Statistics
Matches: 312, Mismatches: 39, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
101 259 0.83
102 8 0.03
103 3 0.01
104 39 0.12
105 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (101 bp):
GTGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCTAA
TGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAG
Found at i:1638482 original size:28 final size:29
Alignment explanation
Indices: 1638396--1638697 Score: 329
Period size: 28 Copynumber: 10.7 Consensus size: 29
1638386 CAACCAACTT
**
1638396 TTGTGGGCTTTTGAAAGGGTTG-CACCAAC
1 TTGTGGGCTTTTGAAA-GGTTGCCACTGAC
*
1638425 TTGTGTGC-TTTG-AAGGTTGCCACTGAC
1 TTGTGGGCTTTTGAAAGGTTGCCACTGAC
* *
1638452 TTGTGGGC-TTTGAAAAAG-TGCCACTAAC
1 TTGTGGGCTTTTG-AAAGGTTGCCACTGAC
* * *
1638480 TTGTGGGCTTTTGAAAAGATGCCACTAAC
1 TTGTGGGCTTTTGAAAGGTTGCCACTGAC
1638509 TTGTGGGCTTTTG-AAGGTTGCCACTGAC
1 TTGTGGGCTTTTGAAAGGTTGCCACTGAC
* * *
1638537 TTGTGGGC-TTTGCAAGGGGTGCCACCGAC
1 TTGTGGGCTTTTG-AAAGGTTGCCACTGAC
1638566 TTGTGGGCTTTTG-AAGGTTGCCACTGAC
1 TTGTGGGCTTTTGAAAGGTTGCCACTGAC
1638594 TTGTGGGCTTTTG-AAGGTTGCCACTGAC
1 TTGTGGGCTTTTGAAAGGTTGCCACTGAC
* *
1638622 TTGTGGGC-TTTGAAAGGGGTGCCACCGAC
1 TTGTGGGCTTTTGAAA-GGTTGCCACTGAC
* * * *
1638651 TTATGGGCTTTTGAAAAGATGCCACTAAC
1 TTGTGGGCTTTTGAAAGGTTGCCACTGAC
*
1638680 TTGTGGG-TTTTGGAAGGT
1 TTGTGGGCTTTTGAAAGGT
1638698 GAGGAATGTC
Statistics
Matches: 236, Mismatches: 26, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
26 5 0.02
27 26 0.11
28 104 0.44
29 90 0.38
30 11 0.05
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (29 bp):
TTGTGGGCTTTTGAAAGGTTGCCACTGAC
Found at i:1638519 original size:57 final size:56
Alignment explanation
Indices: 1638442--1638697 Score: 293
Period size: 57 Copynumber: 4.5 Consensus size: 56
1638432 CTTTGAAGGT
* *
1638442 TGCCACTGACTTGTGGGCTTTGAAAAAG-TGCCACTAACTTGTGGGCTTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTG--AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGA
* ** *
1638499 TGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC-TTTGCAAGGGG
1 TGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAGA
* * *
1638556 TGCCACCGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTG-AAGGT
1 TGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGA
* * *
1638612 TGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTATGGGCTTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTG-AA-GGTTGCCACTGACTTGTGGGCTTTTGAAAAGA
* *
1638670 TGCCACTAACTTGTGGGTTTTGGAAGGT
1 TGCCACTGACTTGTGGGCTTT-GAAGGT
1638698 GAGGAATGTC
Statistics
Matches: 172, Mismatches: 19, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
55 4 0.02
56 29 0.17
57 106 0.62
58 32 0.19
59 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (56 bp):
TGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGA
Found at i:1638546 original size:85 final size:85
Alignment explanation
Indices: 1638396--1638697 Score: 423
Period size: 85 Copynumber: 3.6 Consensus size: 85
1638386 CAACCAACTT
* * * *
1638396 TTGTGGGCTTTTGAAAGGGTTG-CACCAACTTGTGTGC-TTTGAAGGTTGCCACTGACTTGTGGG
1 TTGTGGGCTTTTGAAA-AGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGG
** **
1638459 CTTTGAAAAAGTGCCACTAAC
65 CTTTGAAAGGGTGCCACCGAC
1638480 TTGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1 TTGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
*
1638545 TTTGCAAGGGGTGCCACCGAC
66 TTTG-AAAGGGTGCCACCGAC
* * *
1638566 TTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1 TTGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
1638630 TTTGAAAGGGGTGCCACCGAC
66 TTTGAAA-GGGTGCCACCGAC
*
1638651 TTATGGGCTTTTGAAAAGATGCCACTAACTTGTGGG-TTTTGGAAGGT
1 TTGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTT-GAAGGT
1638698 GAGGAATGTC
Statistics
Matches: 195, Mismatches: 17, Indels: 10
0.88 0.08 0.05
Matches are distributed among these distances:
83 3 0.02
84 31 0.16
85 112 0.57
86 49 0.25
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (85 bp):
TTGTGGGCTTTTGAAAAGATGCCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGC
TTTGAAAGGGTGCCACCGAC
Found at i:1640186 original size:19 final size:19
Alignment explanation
Indices: 1640162--1640212 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1640152 CATTCGGACC
*
1640162 CTTTTTGTTGTTTTTT-TTT
1 CTTTTTGTT-TTTTTTGTCT
1640181 CTTTTTGTTTTTTTTGTCT
1 CTTTTTGTTTTTTTTGTCT
1640200 CTTTTT-TTTTTTT
1 CTTTTTGTTTTTTT
1640213 ACAGAGGATG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.43
19 17 0.57
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (19 bp):
CTTTTTGTTTTTTTTGTCT
Found at i:1640190 original size:16 final size:18
Alignment explanation
Indices: 1640169--1640212 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
1640159 ACCCTTTTTG
1640169 TTGTTTTTTTT-TCT-TT
1 TTGTTTTTTTTGTCTCTT
1640185 TTGTTTTTTTTGTCTCTT
1 TTGTTTTTTTTGTCTCTT
1640203 TT-TTTTTTTT
1 TTGTTTTTTTT
1640213 ACAGAGGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.42
17 11 0.42
18 4 0.15
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (18 bp):
TTGTTTTTTTTGTCTCTT
Found at i:1655463 original size:13 final size:13
Alignment explanation
Indices: 1655422--1655475 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1655412 CCGTTACAAG
1655422 CAATGTATCGATA
1 CAATGTATCGATA
*
1655435 CAA--T-TCCA-A
1 CAATGTATCGATA
1655444 C-ATGTATCGATA
1 CAATGTATCGATA
1655456 CAATGTATCGATA
1 CAATGTATCGATA
*
1655469 CATTGTA
1 CAATGTA
1655476 CTATTATCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
8 1 0.03
9 2 0.06
10 4 0.12
11 4 0.12
12 2 0.06
13 20 0.61
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1655563 original size:19 final size:19
Alignment explanation
Indices: 1655519--1655591 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1655509 CTGCCAGTTT
* **
1655519 CATGTATCGATATAATTGTC
1 CATGTATCGATACAA-TGAA
1655539 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1655558 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
1655579 -ATGTATCGATACA
1 CATGTATCGATACA
1655592 TCTGGGTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
19 18 0.38
20 28 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1657974 original size:21 final size:22
Alignment explanation
Indices: 1657950--1657990 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1657940 AGTGAAAAAC
*
1657950 AAGAAATTTGTA-AAAGATTTG
1 AAGAAATTTGAAGAAAGATTTG
*
1657971 AAGAATTTTGAAGAAAGATT
1 AAGAAATTTGAAGAAAGATT
1657991 GATAGGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.32
Consensus pattern (22 bp):
AAGAAATTTGAAGAAAGATTTG
Found at i:1658096 original size:13 final size:13
Alignment explanation
Indices: 1658078--1658108 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1658068 AAATAGTACC
1658078 CAATGTATCGATA
1 CAATGTATCGATA
1658091 CAATGTATCGATA
1 CAATGTATCGATA
1658104 CAATG
1 CAATG
1658109 AATGTTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1667630 original size:13 final size:13
Alignment explanation
Indices: 1667612--1667636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1667602 AGAAGAGGAA
1667612 AAAGAAAAAAGAG
1 AAAGAAAAAAGAG
1667625 AAAGAAAAAAGA
1 AAAGAAAAAAGA
1667637 AAACAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAGAG
Found at i:1672418 original size:20 final size:20
Alignment explanation
Indices: 1672393--1672430 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1672383 TCAAAAACCC
1672393 AGAATGTATCGATACAATAA
1 AGAATGTATCGATACAATAA
*
1672413 AGAATGTATCGATGCAAT
1 AGAATGTATCGATACAAT
1672431 TGGATCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (20 bp):
AGAATGTATCGATACAATAA
Found at i:1672453 original size:51 final size:50
Alignment explanation
Indices: 1672364--1672530 Score: 212
Period size: 51 Copynumber: 3.3 Consensus size: 50
1672354 ATTTAACTGG
*
1672364 ATGTATCGATATATTTAGG-TCAAAAACCCAGAATGTATCGATACAATAAAGA
1 ATGTATCGATACA-TT-GGATC-AAAACCCAGAATGTATCGATACAATAAAGA
* * * *
1672416 ATGTATCGATGCAATTGGATCAAAACCTAGAATGTATCGACACAATGAAGA
1 ATGTATCGATAC-ATTGGATCAAAACCCAGAATGTATCGATACAATAAAGA
* * *
1672467 ATATATCGATACATTGGATCAAAACCCAAAATTTATCGATACAATAAA-A
1 ATGTATCGATACATTGGATCAAAACCCAGAATGTATCGATACAATAAAGA
1672516 ATGTATCGATACATT
1 ATGTATCGATACATT
1672531 TTCTTTTTAG
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
49 15 0.15
50 31 0.31
51 39 0.39
52 14 0.14
53 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (50 bp):
ATGTATCGATACATTGGATCAAAACCCAGAATGTATCGATACAATAAAGA
Found at i:1672594 original size:20 final size:20
Alignment explanation
Indices: 1672569--1672619 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1672559 ATAAGGTCCA
1672569 GTATCGATACATTCACTAAT
1 GTATCGATACATTCACTAAT
* *
1672589 GTATCGATGCATTCACTCAT
1 GTATCGATACATTCACTAAT
*
1672609 GTATCAATACA
1 GTATCGATACA
1672620 AATTATAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
GTATCGATACATTCACTAAT
Found at i:1674247 original size:21 final size:21
Alignment explanation
Indices: 1674222--1674272 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
1674212 TTCTACAATT
* *
1674222 TGTATCGATAAAATAAGTTAA
1 TGTATCGATAAAATAACTGAA
* *
1674243 TGTATCGA-GACATAACTGAA
1 TGTATCGATAAAATAACTGAA
1674263 TGTATCGATA
1 TGTATCGATA
1674273 TTGGACCTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (21 bp):
TGTATCGATAAAATAACTGAA
Found at i:1682190 original size:19 final size:19
Alignment explanation
Indices: 1682166--1682231 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 19
1682156 ATAATGATAA
1682166 ATGTATCGATACAAAACTC
1 ATGTATCGATACAAAACTC
* *
1682185 ATGTATCCATGC---A-TC
1 ATGTATCGATACAAAACTC
* *
1682200 --GTATCAATACAAAACTT
1 ATGTATCGATACAAAACTC
1682217 ATGTATCGATACAAA
1 ATGTATCGATACAAA
1682232 TTGTAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
13 8 0.23
15 2 0.06
16 2 0.06
17 1 0.03
19 22 0.63
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.29
Consensus pattern (19 bp):
ATGTATCGATACAAAACTC
Found at i:1685634 original size:15 final size:16
Alignment explanation
Indices: 1685614--1685646 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1685604 TCATACTAAG
1685614 TTTC-TTCTTTCTCTT
1 TTTCTTTCTTTCTCTT
1685629 TTTCTTTTCTTTCTCTT
1 TTTC-TTTCTTTCTCTT
1685646 T
1 T
1685647 CCTTCTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
17 12 0.75
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTCTTTCTTTCTCTT
Found at i:1689698 original size:28 final size:28
Alignment explanation
Indices: 1689658--1689730 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
1689648 AATAAAAATA
*
1689658 AGGTTGGAGTATCCCCTCGAAAATAACG
1 AGGTTAGAGTATCCCCTCGAAAATAACG
*
1689686 -GGATTAGAGTATCCCTTCGAAAATAACG
1 AGG-TTAGAGTATCCCCTCGAAAATAACG
*
1689714 AGGTTAAAGTATCCCCT
1 AGGTTAGAGTATCCCCT
1689731 AGATAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 2 0.05
28 35 0.90
29 2 0.05
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (28 bp):
AGGTTAGAGTATCCCCTCGAAAATAACG
Found at i:1699679 original size:53 final size:52
Alignment explanation
Indices: 1699558--1699718 Score: 213
Period size: 53 Copynumber: 3.1 Consensus size: 52
1699548 AAAAGAATTT
1699558 TATATTAAATCCTAAATTACTATTTAAAAAATAATAAAAA--TTAAAACT-TT-
1 TATATTAAATCCTAAATTACTATTT-AAAAATAATAAAAATTTTAAAA-TATTA
*
1699608 TATATTAAATCCTAAATTACAATTTAAAAATAATAAAATATTTTAAAATATTA
1 TATATTAAATCCTAAATTACTATTTAAAAATAATAAAA-ATTTTAAAATATTA
* * * *
1699661 TATATTAAATCTTGAATTATTATTTAAAAATAATAAAAAATTTAAAAATATTA
1 TATATTAAATCCTAAATTACTATTTAAAAATAAT-AAAAATTTTAAAATATTA
1699714 TATAT
1 TATAT
1699719 ATGTAATTTG
Statistics
Matches: 99, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
49 13 0.13
50 25 0.25
51 1 0.01
52 8 0.08
53 48 0.48
54 4 0.04
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (52 bp):
TATATTAAATCCTAAATTACTATTTAAAAATAATAAAAATTTTAAAATATTA
Found at i:1701007 original size:97 final size:97
Alignment explanation
Indices: 1700914--1701120 Score: 279
Period size: 97 Copynumber: 2.1 Consensus size: 97
1700904 GGAAGAATAA
* * * * *
1700914 GGTTGGAGTATCCCCGACGATGATAATTTAGGCAAAAATAAGATTTATATCGTGACAAGTTTAAA
1 GGTTGGAGTATCCCCGACAATGACAATTTAAGCAAAAATAAGATTTAAATCGTAACAAGTTTAAA
* *
1700979 AACGATATTGGAGTATCCTCTCAAAAGAATGG
66 AACGAGATTGGAGTATCCCCTCAAAAGAATGG
** * *
1701011 GGTTGGAGTATCGTCGACAATGGCAATTTAAGCAAAAATAAGATTTAAATCTTAACAAGTTTAAA
1 GGTTGGAGTATCCCCGACAATGACAATTTAAGCAAAAATAAGATTTAAATCGTAACAAGTTTAAA
* ***
1701076 AACGAGGTTGGAGTATCCCCTTGGAAGAATGG
66 AACGAGATTGGAGTATCCCCTCAAAAGAATGG
1701108 GGTTGGAGTATCC
1 GGTTGGAGTATCC
1701121 TCAATAAATA
Statistics
Matches: 94, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.28
Consensus pattern (97 bp):
GGTTGGAGTATCCCCGACAATGACAATTTAAGCAAAAATAAGATTTAAATCGTAACAAGTTTAAA
AACGAGATTGGAGTATCCCCTCAAAAGAATGG
Found at i:1702096 original size:20 final size:20
Alignment explanation
Indices: 1702071--1702127 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 20
1702061 TACTGCCAGT
1702071 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACATTTG
*
1702091 TTCATGTATCGATACA-ATG
1 TTCATGTATCGATACATTTG
**
1702110 AACATGTATCGATACATT
1 TTCATGTATCGATACATT
1702128 GTATCGATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
TTCATGTATCGATACATTTG
Done.